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MCB 2020 > 1.5 Enzymes > Flashcards

1.5 Enzymes Flashcards

1
Q

Hwo does the binding of enzymes to transition states compare to binding of substrate or product?

A
  • Enzymes bind transition states best
  • Enzyme active sites are complimentary to the transition state of the reaction so they bind better than the substrates
  • Additional interactions also lower activation barrier
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2
Q
A
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3
Q

How do enzymes lower the activation energy?

A
  • Enzyme catalysed reactions are characterised by the formation of acomplex between enzyme and substrate
  • Stabilisation of the transition state through tight binding of the enzyme
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4
Q

What are the three catalytic mechanisms enzymes may take?

A
  • Acid base catalysis - give and take protons
  • Covalent catalysis - change reaction paths
  • metal ion catalysis - use redox cofactors, pKa shifters
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5
Q

Why are enzymes so important in metabolism?

A

Living organisms must be able to catalyse the conversion of carbon fuel sources into cellular energy (ATP) in an approopriate time scale

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6
Q

What causes phenylketonuria?

A

A deficiency in the enzyme phenylalanine hydroxylase.

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7
Q

What are cofactors and coenzymes?

A
  • additional chemical components that enzymes require for activity
  • Either small inorganic molecules called cofactors eg Mg2+, K
  • More complex molecules called coenzymes that transiently carry funcitonal groups during catalysis of a reaction
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8
Q

What are some of the most common types of enzymes?

A
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9
Q

What are kinases?

A

They catalyse the phosphoryl transfer from one molecule (usually ATP) to another for example hexokinase

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10
Q

What is the phosphorylase enzyme?

A

Catalyses the covalent addition of inorganic phosphate (Pi) to a moelcules

Eg glycogen phosphorylase

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11
Q

What is the phosphatase enzyme?

A

It catalyses the cleavage of a phosphate to yield the dephosphorylated product and Pi

Example glucose-6-phosphatase

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12
Q

What is the dehydrogenase enzyme?

A

It catalyses a redox reaction commonly using NADH/NAD+, NADPH/NADP+ or FADH2/FAD as cofactors

Example glyceraldehyde-3-phosphate dehydrogenase

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13
Q

What does the mutase enzyme do?

A

Catalyses the shift of a phosphoryl group from one atom to another within the same molecule

Example phosphoglycerate mutase

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14
Q

What does the isomerase enzymes do?

A

Catalyses the conversion of one isomer to another, triose phosphate isomerase

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15
Q

What does the hydratase enzyme type do?

A

Catalyses the addition/removal of water e.g enolase

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16
Q

What does synthase enzyme do?

A

Catalyses the synthesis of a product.

Example citrate synthase

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17
Q
A
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18
Q
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19
Q

What is the binding free energy?

A

The difference between the activation energies of the uncatalysed and catalysed reactions caused by the enzyme binding the transition state

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20
Q

WHy does the rate of reaction decrease over time for enzyme substrate reaction?

A
  • S is depleted by conversion to products
  • The reaciton is reversible so as [P] increases the rate of the reverse reaction increases
  • The enzyme may be unstable under the reaction conditions
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21
Q

What is the relationship between the initial rate of reaction and the concentration of enzyme?

A
22
Q

How do you work out what the Km for an enzyme is?

A
  1. Determine Vo at varying [S]
  2. Plot Vo as a function of [S] and see the concentration of substrate at which Vo is half of Vmax
23
Q

In michaelis menten theory what is the form of the enzyme substrate reaction?

A
24
Q

What are the four assumptions used in michaelis menten theory?

A
25
Q

What is the michaelis menten equation?

A
26
Q

What is the rate determining step in michaelis menten kinetics?

A

The conversion of ES to E and P

27
Q

What is the steady state assumption for michaelis menten kinetics?

A

Vo represents the steady state where [ES] remains constant.

Right when the reaction starts the rate of formation of ES = the rate of ES breakdown

28
Q

How does steady state assumption impact equilibria?

A
29
Q

What equation is used for the double reciprocal plot?

A
30
Q

What are the axis of each double reciprocal plot?

A

x axis is 1/[S]

the y axis is 1/Vo

31
Q

What is on the intercepts of the double reciprocal plots?

A

X intercepts represents the -1/Km

Y intercept is 1/Vmax

32
Q

What is the slope of the double reciprocal plot?

A

Km/Vmax

33
Q

What is the relationship between Kd and Km?

A

Km has the Steady State assumption and takes account of the catalytic step

34
Q

What is the turnover number and where does it come from?

A
  • In michaelis menten kinetics K2 is the rate constant for the rate limiting step
  • Called Kcat or the turnover number
  • Means the number of molecules of substrate converted to product (S to P) per unit time per enzyme molecule saturated with substrate (when [ES] = [Et]
35
Q

What is the specifity constant?

A
  • It is Kcat/Km
  • Defined as the rate constant for the conversion of E+S to E+P
  • It reflects both substrate affinity and catalytic efficiency, high value indicates more efficient use of the substrate
36
Q

What are irreversible inhibitors defined as?

A

They bind covalently to the active site, destroy a functional group essential for enzyme activity, or form a stable non covalent complex with the enzyme (suicide inhibitors)

37
Q

What are reversible inhibitors defined as?

A

They bind reversibly to the enzymes and inhibit the enzyme either by competitive, uncompetitive or mixed modes of inhibition

38
Q

What changes in the michaelis menten equation are seen due to competitive inhibition?

A

There is an alpha constant added in front of Km

39
Q

How does the double reciprocal plot change for a competitive inhibition?

A

As alpha increase the gradient increases so x intercept gets closer to the right

40
Q

How does the michaelis menten equation change with uncompetitive inhibition?

A

And alpha’ constant gets added in front of [S]

41
Q

How does the shape of the double reciprocal plot change with uncompetitive inhibition?

A

The line gets translated up the y axis with increasing alpha prime

42
Q

How does the michaelis menten equation change with the mixed inhibition?

A

alpha gets added to Km and alpha’ to [S]

43
Q

How does mixed inhibition change the shape of the double reciprocal plot?

A
44
Q

What do allosteric enzymes do?

A
  • Regulate metabolic pathways by changing activity in response to chagnes in the concentration of molecules around them
  • Allosteric enzymes are regulated by compounds called allosteric modulators or allosteric effectors
45
Q

What are the types of allosteric modulators and how do they bind?

A
  • Positive modulators’ activate and ‘negative modulators’ inhibit allosteric enzymes
  • Modulators bind reversibly and non-covalently to the enzyme – they can ‘come and go’
46
Q

How does a positive allosteric regulator work?

A
47
Q

How do allosteric regulators change the shape of Vo and [S] graph?

A
  • As S (e.g.forATCase, S is Asp or carbamyl phosphate) binds, there is a transition from the T state to the R state to give a sigmoidal V0 versus S plot
  • A relatively small increase in S on the steep part of the curve causes a relatively large increase in V0
48
Q

What is the role of ATCase?

A

It catalyses the first step in the E coli pathway to produce the nucleotides UTP and finally CTP

49
Q

How is ATCase seen to be an allosteric enzyme?

A
  • CTP inhibits ATCase at high levels so its a negative modulator
  • HIgh ATP levels in the bacteria indicate the growth of the cell and the need for more CTP, so ATP is a positive modulator
50
Q

What is the structure of ATCase?

A

It has complex quaternary structure of 12 subunits

  • 6 catalytic subunits, arranged as 2 x trimeric complexes. The catalytic subunits function cooperatively
  • 6 regulatory subunits, arranged as 3x dimeric complexes
51
Q

How does the shape of the Vo vs [S] plot change with modulators?

A
  • As ATP increases, the V0 vs [S] plot becomes more hyperbola-like
  • As CTP increases, the V0 vs [S] plot shifts to the right – the substrate concentration at 1⁄2 V0 (K0.5) increases

MCB 2020 (38 decks)

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